inst/tests/test-S4.R

In openanalytics/gread: Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

# context("S4 Compatability")

# ## S4 class definitions to test
# setClass("Data.Table", contains="data.table")
# setClass("S4Composition", representation(data="data.table"))

# test_that("data.table can be a parent class", {
#   ids <- sample(letters[1:3], 10, replace=TRUE)
#   scores<- rnorm(10)
#   dt <- data.table(id=ids, score=scores)
#   dt.s4 <- new("Data.Table", data.table(id=ids, score=scores))

#   expect_true(isS4(dt.s4))
#   expect_true(inherits(dt.s4, 'data.table'))

#   ## pull out data from S4 as.list, and compare to list from dt
#   dt.s4.list <- dt.s4@.Data
#   names(dt.s4.list) <- names(dt.s4)
#   expect_identical(dt.s4.list, as.list(dt), info="Underlying data not identical")
# })

# test_that("simple S4 conversion-isms work", {
#   df = data.frame(a=sample(letters, 10), b=1:10)
#   dt = as.data.table(df)
#   expect_equal(as(df, 'data.table'), dt)
#   expect_identical(as(dt, 'data.frame'), df)
# })

# test_that("data.table can be used in an S4 slot", {
#   ## A class with a data.table slot
#   dt <- data.table(a=sample(letters[1:3], 10, replace=TRUE), score=rnorm(10))
#   dt.comp <- new("S4Composition", data=dt)
#   expect_equal(dt.comp@data, dt)
# })

# test_that("S4 methods dispatch properly on data.table slots", {
#   ## Make toy accessor functions and compare results against normal data.table
#   ## access
#   dt <- data.table(a=sample(letters[1:3], 10, replace=TRUE), score=rnorm(10))
#   dt.comp <- new("S4Composition", data=dt)
#   setGeneric("dtGet", function(x, what) standardGeneric("dtGet"))
#   setMethod("dtGet", c(x="S4Composition", what="missing"),
#             function(x, what) {
#               x@data
#             })
#   setMethod("dtGet", c(x="S4Composition", what="ANY"),
#             function(x, what) {
#               x@data[[what]]
#             })

#   expect_equal(dtGet(dt.comp), dt, label='actually')
#   expect_identical(dtGet(dt.comp, 1), dt[[1]])
#   expect_identical(dtGet(dt.comp, 'b'), dt$b)
# })